4Y93

Crystal structure of the PH-TH-kinase construct of Bruton's tyrosine kinase (Btk)

  • Classification: TRANSFERASE
  • Organism(s): Bos taurus
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2015-02-16 Released: 2015-03-18 
  • Deposition Author(s): Wang, Q., Kuriyan, J.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Howard Hughes Medical Institute (HHMI), Cancer Research Institute

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Autoinhibition of Bruton's tyrosine kinase (Btk) and activation by soluble inositol hexakisphosphate.

Wang, Q.Vogan, E.M.Nocka, L.M.Rosen, C.E.Zorn, J.A.Harrison, S.C.Kuriyan, J.

(2015) Elife 4

  • DOI: 10.7554/eLife.06074
  • Primary Citation of Related Structures:  
    4Y93, 4Y94, 4Y95, 4XI2

  • PubMed Abstract: 
  • Bruton's tyrosine kinase (Btk), a Tec-family tyrosine kinase, is essential for B-cell function. We present crystallographic and biochemical analyses of Btk, which together reveal molecular details of its autoinhibition and activation. Autoinhibited Btk adopts a compact conformation like that of inactive c-Src and c-Abl ...

    Bruton's tyrosine kinase (Btk), a Tec-family tyrosine kinase, is essential for B-cell function. We present crystallographic and biochemical analyses of Btk, which together reveal molecular details of its autoinhibition and activation. Autoinhibited Btk adopts a compact conformation like that of inactive c-Src and c-Abl. A lipid-binding PH-TH module, unique to Tec kinases, acts in conjunction with the SH2 and SH3 domains to stabilize the inactive conformation. In addition to the expected activation of Btk by membranes containing phosphatidylinositol triphosphate (PIP3), we found that inositol hexakisphosphate (IP6), a soluble signaling molecule found in both animal and plant cells, also activates Btk. This activation is a consequence of a transient PH-TH dimerization induced by IP6, which promotes transphosphorylation of the kinase domains. Sequence comparisons with other Tec-family kinases suggest that activation by IP6 is unique to Btk.


    Organizational Affiliation

    Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Non-specific protein-tyrosine kinase,Non-specific protein-tyrosine kinaseA446Bos taurusMutation(s): 7 
Gene Names: BTK
EC: 2.7.10.2
Find proteins for Q3ZC95 (Bos taurus)
Explore Q3ZC95 
Go to UniProtKB:  Q3ZC95
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
746
Query on 746

Download Ideal Coordinates CCD File 
C [auth A]4-tert-butyl-N-[2-methyl-3-(4-methyl-6-{[4-(morpholin-4-ylcarbonyl)phenyl]amino}-5-oxo-4,5-dihydropyrazin-2-yl)phenyl]benzamide
C34 H37 N5 O4
JIFCFQDXHMUPGP-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
746IC50:  1.899999976158142   nM  BindingDB
746IC50:  8   nM  BindingDB
746Kd:  1.5   nM  BindingDB
746IC50:  150   nM  BindingDB
746IC50:  81   nM  BindingDB
746IC50:  0.6100000143051147   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.328α = 90
b = 78.647β = 90
c = 157.569γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-02-16 
  • Released Date: 2015-03-18 
  • Deposition Author(s): Wang, Q., Kuriyan, J.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI091580
Howard Hughes Medical Institute (HHMI)United States--
Cancer Research InstituteUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-18
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Advisory, Author supporting evidence, Derived calculations, Source and taxonomy, Structure summary
  • Version 1.2: 2019-11-20
    Changes: Author supporting evidence